It’s only happening for one subject, right? nu_correct isn’t actually a freesurfer tool, it’s an mni tool. I would try to troubleshoot this by installing a newer version of minc for osx: http://packages.bic.mni.mcgill.ca/minc-toolkit/MacOSX/minc-toolkit-1.9.16-20180117-Darwin-10.8-x86_64.dmg

 

Then, set the following BEFORE sourcing freesurfer and try rerunning the failed recon:

 

export MINC_BIN_DIR=/opt/minc/1.9.16/bin

export MINC_LIB_DIR=/opt/minc/1.9.16/lib

 

best

Andrew

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 19, 2019 at 4:14 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error

 

        External Email - Use Caution        

Hi Andrew,

 

I am on a mac pro running Sierra 10.12.6

 

Best,

Daniel Callow

PhD Student, Neuroscience and Cognitive Science

Exercise for Brain Health Lab

University of Maryland, College Park

ddcc2442@gmail.com

443-254-6298

 

 

On Tue, Mar 19, 2019 at 2:40 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi Daniel, I’ve never seen this error before. I assume you’re on a mac – what version are you using?

Andrew

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Daniel Callow <ddcc2442@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 19, 2019 at 10:45 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all error

 

        External Email - Use Caution        

Hello,

I am trying to run recon-all on a dataset and am running into errors with one of my subjects. 

 

I get an error at the following point

--------------------------------------------------------

Iteration 1 Tue Mar 19 10:11:08 EDT 2019

nu_correct -clobber ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ -iterations 1000 -distance 50

[administrator@hlhp-105.umd.edu:/Volumes/DANIEL/freesurfer/Ex.AES118/mri/] [2019-03-19 10:11:09] running:

  /Applications/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.40972/0/ ./tmp.mri_nu_correct.mni.40972/nu0.mnc ./tmp.mri_nu_correct.mni.40972/nu1.imp

 

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

Processing:.................................................................Done

ncvarget: ncid 4; varid 6: Argument list too long

miicv_get: MINC package entry point

nu_estimate_np_and_em: crashed while running mincmath (termination status=768)

nu_correct: crashed while running nu_estimate_np_and_em (termination status=768)

ERROR: nu_correct

Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64

 

recon-all -s Ex.AES118 exited with ERRORS at Tue Mar 19 10:11:18 EDT 2019

 

For more details, see the log file /Volumes/DANIEL/freesurfer/Ex.AES118/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 

Any help you can provide for troubleshooting would be greatly appreciated.

Daniel Callow

PhD Student, Neuroscience and Cognitive Science

Exercise for Brain Health Lab

University of Maryland, College Park

ddcc2442@gmail.com

443-254-6298

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